As far as I know SFALL reads PDB files - I dont think there is an option
to input fractional coordinates..
I suspect it thinks everything is displaced one space to the left or
right ..
Can you run pdbset xyzin now.pdb xyzout now+.pdb
end
and see if there is any difference?
When I run the map correlation task which does this the answers look
sort of sensible..
Data line--- MODE ATMMAP RESMOD
Data line--- grid 130 140 170
Data line--- symmetry 'P 1'
....
fractional coordinates 0.49431 1.19518 0.40395
9N GLN 34-11.0320 40.7750 20.4450 0.50 12.61 3
fractional coordinates 0.38022 1.19991 0.40616
10CA GLN 34-12.3450 40.1470 20.3370 0.50 12.12 2
fractional coordinates 0.34151 1.18372 0.40401
11C GLN 34-12.3150 38.6620 20.7240 0.50 12.77 2
fractional coordinates 0.32789 1.15251 0.41170
First 10 atoms of sorted file in asym unit -
10.48580 0.43335 0.16420 713.64 0.50 2 33CD1 LEU
Eleanor
Adam Ralph wrote:
Hi Pietro,
It looks as though SFALL thinks you have fractional coords and
has coverted them into orthog ones. Does the PDB have a CRYST1 and
SCALEi cards?
Adam
On Thu, 24 Apr 2008, Pietro Roversi wrote:
Dear everyone,
I am using sfall in "MODE ATMMAP RESMOD" to compute a
tagged map with
which to score a model against a map. The input PDB is OK and regularly
read by all programs - but sfall seems to interpret the coordinates
wrongly (see the list of the first 10 atoms coordinates that the program
outputs, both in orthogonal and fractional):
First 10 atoms of atsort - orthog coordinates
1N CYS 140283.0180251.2380115.7960 1.00 500.00 3
fractional coordinates 1.57127 1.39484 0.64288
First 10 atoms of atsort - orthog coordinates
2CA CYS 140281.9190250.4390115.2740 1.00 500.00 2
fractional coordinates 1.56517 1.39040 0.63998
3C CYS 140280.7020251.2870114.8740 1.00 500.00 2
fractional coordinates 1.55842 1.39511 0.63776
4O CYS 140279.7890250.8050114.1860 1.00 500.00 4
fractional coordinates 1.55335 1.39243 0.63394
5CB CYS 140281.5250249.4400116.3580 1.00 500.00 2
fractional coordinates 1.56299 1.38485 0.64600
6SG CYS 140280.3360248.2280115.8470 1.00 500.00 5
fractional coordinates 1.55638 1.37813 0.64317
7N SER 141280.6900252.5440115.3270 1.00 500.00 3
fractional coordinates 1.55835 1.40209 0.64028
8CA SER 141279.5620253.4720115.1380 1.00 500.00 2
fractional coordinates 1.55209 1.40724 0.63923
9CB SER 141279.7800254.7110116.0260 1.00 500.00 2
fractional coordinates 1.55330 1.41412 0.64416
10OG SER 141280.9710255.4130115.6440 1.00 500.00 4
fractional coordinates 1.55991 1.41802 0.64204
11C SER 141279.3470253.9090113.6680 1.00 500.00 2
fractional coordinates 1.55089 1.40967 0.63107
First 10 atoms of sorted file in asym unit -
10.55639 0.64317 0.37813 699.89 1.00 5 102SG
CYS
10.56299 0.64600 0.38485 599.89 1.00 2 102CB
CYS
10.56517 0.63998 0.39040 299.89 1.00 2 102CA
CYS
10.55335 0.63394 0.39243 499.89 1.00 4 102O
CYS
10.57127 0.64288 0.39484 199.89 1.00 3 102N
CYS
10.55842 0.63776 0.39511 399.89 1.00 2 102C
CYS
10.55835 0.64028 0.40209 799.89 1.00 3 103N
SER
10.55209 0.63923 0.40724 899.89 1.00 2 103CA
SER
10.55330 0.64416 0.41412 999.89 1.00 2 103CB
SER
10.55991 0.64204 0.41802 1099.89 1.00 4 103OG
SER
As a result of course the tagged map is completely screwed.
Has anyone encountered this problem and if so how did they solve it? I
would rather avoid digging into the code if I can!
Best regards
Pietro
--
Pietro Roversi
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3ER, England UK
Tel. 0044-1865-275385
